【Objective】 Nitrification, an important component of nitrogen cycling, has the potential to influence soil nitrogen availability. As a result, it will lead to ecological and environmental issues such as eutrophication, and greenhouse gas (nitrous oxide) emissions. The objective of this study was to explore the effect of Chinese milk vetch incorporation on the gene abundance of ammonia-oxidizing microorganisms in red paddy soil under a rice-Chinese milk vetch planting system. 【Method】 In a field experiment, five fertilization treatments were applied, including Chinese milk vetch incorporation (G), 100% chemical fertilizer (C), Chinese milk vetch incorporation + 100% chemical fertilizer (GC), and Chinese milk vetch incorporation + 20% chemical fertilizer reduction (GCT20), with a no fertilization treatment serving as the control (CK). Real-time quantitative PCR was used to determine the abundance of ammonia-oxidizing archaea (AOA), ammonia-oxidizing bacteria (AOB), and comammox Nitrospira Clade A and Clade B in each treatment. 【Result】 The results showed that Chinese milk vetch incorporation increased soil organic carbon and total nitrogen content compared with CK, while the 100% chemical fertilizer treatment showed no significant effect. There was no significant difference in AOA and Clade B abundance among all the treatments, indicating a weak response to nitrogen inputs from both chemical fertilizers and green manure. However, both the sole application of chemical fertilizer and its combination with Chinese milk vetch incorporation significantly increased the abundance of AOB and Clade A. Additionally, Chinese milk vetch incorporation alone had no significant effect on AOB and Clade A, suggesting their sensitivity to chemical fertilizer, but resistance to green manure nitrogen input. Furthermore, gene abundance of all ammonia-oxidizing microorganisms showed a similar trend across growth stages, with higher abundance observed during the mature stage followed by the booting stage and then the tillering stage. This suggests that growth stage and oxygen concentration are key factors influencing the growth of these microorganisms in paddy soils. 【Conclusion】 Growth stage is a key factor affecting the abundance of ammonia-oxidizing microorganisms in paddy soils. Additionally, Chinese milk vetch incorporation had a weaker promotion effect on AOB and Clade A abundance compared to chemical fertilizer, potentially contributing to nitrogen retention and stability in paddy soils.